Found this great site via a google search and I've got a question for you.

I currently have a 20user BES server which comprises 14 users in my company and 5 users from our sister company downstaires.

I want to create a new office infrastructure which will split us up into seperate domains. Unfortunatley the problem in doing this is the BES server that both companies use (because we're on the same Exchange server currently). When we give them their own Exchange server is there a way to have the BES connect to 2 seperate domains/Exchange servers to get email?

Depending on your total user count, and I assume it's more than 20, you might want to set up a different default domain for those users in Exchange, and keep the Exchange servers in the same AD domain/forest.